Silicon IC unravels DNA's spiral for easy reading

Portland, Ore.-Researchers at Purdue University have succeeded in unraveling strands of DNA into an easy-to-ready linear "tape," potentially a first step toward one day creating computers based on DNA, according to the team.

"We wanted to be able to extend DNA strands, to stretch them out so that we could read what's on [them]" said Albena Ivanisevic, an assistant professor of biomedical engineering. "There are a variety of DNA computing strategies, but for any of them you need to have the strand extended, and in a specific location." He performed the work with Purdue physics graduate student Dorjderem Nyamjav.

The two patterned 100-nanometer-wide lines of a positively charged polymer (polyallylamine hydrochloride) atop a 1-cm-square silicon (SiOx) substrate using an atomic-force microscope and a cantilever. Via the dip-pen technique (www.eetimes. com/at/n/news/ OEG20030707S0060), the microscope was used like a quill to dip and write nanolithographic lines at the nanometer scale. (A single DNA molecule is about 2 nm wide, the width of about 20 hydrogen atoms.) A tiny droplet of water attached to the tip enables the deposition material to slide off onto the substrate.

The lines' electrostatic charge (positive) attracted the oppositely charged DNA molecules (negative), enabling them to be tethered at one end. The researchers then located the strands and uncoiled them along the template's lines using a technique chemists call molecular combing.

"Because they were charged, we were able to direct the biological molecules in certain locations," Ivanisevic said.

Purely mechanical

By demonstrating that DNA strands can be laid out linearly, the researchers opened the door to future nanoscale Turing machines that use DNA as tape. When Alan Turing invented the Turing machine-basically a read/write head under which ran a linear tape-he drew inspiration from the German mathematician David Hilbert. Hilbert's formalisms portended a "universal" algorithmic system that could solve any mathematical problem with a purely mechanical process. Geneticists have found a kind of Turing machine using DNA as the tape. However, the spiral shape of the DNA molecules makes it difficult to create a traditional "linear" Turing machine from them. That is the problem tackled by Ivanisevic and Nyamjav, who have precisely unraveled DNA strands along lines of polymer deposited on silicon surfaces.

Next the researchers need a read head, which they plan to implement by running the stands between two electrodes, thereby performing consistent, precise measurements of the codes-Hilbert's "purely mechanical process." "At this point, these are very basic nanofabrication problems," said Ivanisevic. "But you can begin to think about making real molecular devices where DNA is used as a construction material."